PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC10366_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 1321aa    MW: 147399 Da    PI: 7.2448
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC10366_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.20.0005412041229123
                   EEET..TTTEEESSHHHHHHHHHH.T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                   ykC    C++sFs+  +L  H r+ +
  RrC10366_p1 1204 YKCDieGCTMSFSSEKQLSMHKRNiC 1229
                   99********************9877 PP
2zf-C2H214.97.5e-0512291251323
                   ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                   Cp   CgksF ++ +L++H r+H
  RrC10366_p1 1229 CPvkGCGKSFFSHKYLVQHRRVH 1251
                   9999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-161758IPR003349JmjN domain
PROSITE profilePS5118313.6891859IPR003349JmjN domain
PfamPF023757.5E-141952IPR003349JmjN domain
SuperFamilySSF511971.84E-26129176No hitNo description
SMARTSM005581.4E-53198367IPR003347JmjC domain
PROSITE profilePS5118434.235201367IPR003347JmjC domain
SuperFamilySSF511971.84E-26216382No hitNo description
PfamPF023733.8E-38231350IPR003347JmjC domain
Gene3DG3DSA:3.30.160.609.1E-412031226IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003557.112041226IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.21412271256IPR007087Zinc finger, C2H2
SMARTSM003550.002712271251IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-612281255IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012291251IPR007087Zinc finger, C2H2
SuperFamilySSF576672.5E-1012431285No hitNo description
Gene3DG3DSA:3.30.160.608.2E-1012561280IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.80112571286IPR007087Zinc finger, C2H2
SMARTSM003550.001512571281IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012591281IPR007087Zinc finger, C2H2
SuperFamilySSF576671.42E-812751309No hitNo description
Gene3DG3DSA:3.30.160.601.9E-912811309IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.15712871318IPR007087Zinc finger, C2H2
SMARTSM003551.212871313IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012891313IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1321 aa     Download sequence    Send to blast
MSEQSTDVFP WLKSLPVAPE FRPTLAEFQD PIAYIFKIEE EASRYGICKI LPPLPPPSKK  60
TTVSNLNRSL AARASTHDGA CDYDGSPAFA TRQQQVGFCP RKQRPVQRPV WQSGERYSFG  120
EFEAKTKTFE KSYLKRCCGG GRKSQQLSAL EIETLYWRAT VDKPFTVEYA NDMPGSAFIP  180
LSLAAARRRE YGGSDGGTVG ESAWNMRAMA RAEGSLLRFM KEEIPGVTSP MVYVAMMFSW  240
FAWHVEDHDL HSLNYLHMGA GKTWYGVPKD AALAFEEVVR DHGYGGELNP LVTFSTLGEK  300
TTVMSPEVFV KAGIPCCRLV QNPGEFVVTF PRAYHSGFSH GFNCGEASNI ATPEWLRVAK  360
EAAIRRAAIS YPPMVSHLQL LYDYALALGS RVPASIHAKP RSSRLKDKKR SEGERLSKEL  420
FAQNVIHNNE LLCSLGKGSP VALLPQSSSD VSVCSDLRIG SHLSANQEKP IQPKSEDLSP  480
ESNTVCLKET VSVKEKFTSL CGRNINQETM PEAERREKDG AVGLSDQRLF SCVSCGIICF  540
DCVAIVQPKE AAARYLSSAD CSFFSDRTVS SGSANPGQDE RSLVVEPHPQ SMGKRDVGCI  600
YSAPVQSTDH SIMTIDQGTS TASSALGLLA SAYGDSSDSE EEEHKGIDAV ISQNGASSYK  660
TPAFCTDGNE EATADGGTSD HSSERLSCGK GKGVDEGSNG GSASVLKVTL PFVSSSDDDS  720
SRLHVFCLEH AAEVEQQLRP FGGINIMLLC HPEYPRIEAE GKVVAEELGV KHEWSDTEFR  780
NVTREDEETI QAALVNVEAK AGNRDWTVKL SINLSYSAIL SRSPLYSKQM PYNSVIYNMF  840
GRSSPSTSSP TQHQVSGQRS CRQRKYVVGK WCGKVWMSHQ VHPFLLQEDS EGEETERSHL  900
RVEDVSGERL SPCDVSRDAT TMFGRKYSRK RKMRAKAVTR KKLTSFKRED GVSDDTSEDH  960
SYKQQWRRGF GNEEEMSDDS SDPMSDHQQQ QLLKGIRRDK GVREFESDDE VSDRSLGEEY  1020
AARECADSDS STDIDALEDS VYDGHNDDSI HKHPRSKRAK VIRIPVYQQR GNIQASQIGG  1080
DYDSEDDSLE EQEGFSTRKR QTRSTAKRKV KTEIVESPRD TRGRRTLQQS GYRKKIQDLD  1140
PYMEGPSTRL RVRNLKPSRK SSETKPKRGS SNASFSRVVS EEEELEEDDE EEGEEERAAA  1200
ASAYKCDIEG CTMSFSSEKQ LSMHKRNICP VKGCGKSFFS HKYLVQHRRV HSDDRPLKCP  1260
WKGCKMTFKW AWSRTEHIRV HTGERPYHCA EPGCGQTFRF VSDFSRHKKK TGHSAKKTKK  1320
R
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-7563903355Transcription factor jumonji (Jmj) family protein
6ip4_A3e-7563903355Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1927932SRKRKM
2929941KRKMRAKAVTRKK
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018458317.10.0PREDICTED: lysine-specific demethylase REF6-like isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4M0K30.0V4M0K3_EUTSA; Uncharacterized protein
STRINGXP_006404260.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  2. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  3. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  4. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  5. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  6. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]